7V0K

Consensus refinement of human erythrocyte ankyrin-1 complex (Composite map)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Architecture of the human erythrocyte ankyrin-1 complex.

Vallese, F.Kim, K.Yen, L.Y.Johnston, J.D.Noble, A.J.Cali, T.Clarke, O.B.

(2022) Nat Struct Mol Biol 29: 706-718

  • DOI: https://doi.org/10.1038/s41594-022-00792-w
  • Primary Citation of Related Structures:  
    7UZ3, 7UZE, 7UZQ, 7UZS, 7UZU, 7UZV, 7V07, 7V0K, 7V0M, 7V0Q, 7V0S, 7V0T, 7V0U, 7V0X, 7V0Y, 7V19, 8CRQ, 8CRR, 8CRT, 8CS9, 8CSL, 8CSV, 8CSW, 8CSX, 8CSY, 8CT2, 8CT3, 8CTE

  • PubMed Abstract: 

    The stability and shape of the erythrocyte membrane is provided by the ankyrin-1 complex, but how it tethers the spectrin-actin cytoskeleton to the lipid bilayer and the nature of its association with the band 3 anion exchanger and the Rhesus glycoproteins remains unknown. Here we present structures of ankyrin-1 complexes purified from human erythrocytes. We reveal the architecture of a core complex of ankyrin-1, the Rhesus proteins RhAG and RhCE, the band 3 anion exchanger, protein 4.2, glycophorin A and glycophorin B. The distinct T-shaped conformation of membrane-bound ankyrin-1 facilitates recognition of RhCE and, unexpectedly, the water channel aquaporin-1. Together, our results uncover the molecular details of ankyrin-1 association with the erythrocyte membrane, and illustrate the mechanism of ankyrin-mediated membrane protein clustering.


  • Organizational Affiliation

    Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Blood group Rh(CE) polypeptideA [auth K]417Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P18577 (Homo sapiens)
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PHAROS:  P18577
GTEx:  ENSG00000188672 
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UniProt GroupP18577
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ammonium transporter Rh type AB [auth L],
C [auth Q]
409Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q02094 (Homo sapiens)
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PHAROS:  Q02094
GTEx:  ENSG00000112077 
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UniProt GroupQ02094
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ankyrin-1D [auth H]1,881Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P16157 (Homo sapiens)
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PHAROS:  P16157
GTEx:  ENSG00000029534 
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UniProt GroupP16157
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Band 3 anion transport proteinE [auth W],
I [auth O],
J [auth P]
911Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P02730 (Homo sapiens)
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PHAROS:  P02730
GTEx:  ENSG00000004939 
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UniProt GroupP02730
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Protein 4.2F [auth X]691Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P16452 (Homo sapiens)
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PHAROS:  P16452
GTEx:  ENSG00000166947 
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UniProt GroupP16452
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Glycophorin-AG [auth N],
H [auth D]
150Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P02724 (Homo sapiens)
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PHAROS:  P02724
GTEx:  ENSG00000170180 
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UniProt GroupP02724
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJP
Query on AJP

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M [auth Q],
N [auth Q]
Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
PIO (Subject of Investigation/LOI)
Query on PIO

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W [auth P],
X [auth P]
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
PLC
Query on PLC

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R [auth O],
V [auth P]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
CLR
Query on CLR

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K [auth L]
L
O
Q [auth O]
S [auth P]
K [auth L],
L,
O,
Q [auth O],
S [auth P],
U [auth P]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

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P [auth O],
T [auth P]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONcryoSPARC3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references